下载PDF
{"title":"metbridge:代谢酶图谱的综合多组学工具","authors":"Travis Blimkie, Amy Huei-Yi Lee, Robert E.W. Hancock","doi":"10.1002/cpbi.98","DOIUrl":null,"url":null,"abstract":"<p>MetaBridge is a web-based tool designed to facilitate the integration of metabolomics with other “omics” data types such as transcriptomics and proteomics. It uses data from the MetaCyc metabolic pathway database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to map metabolite compounds to directly interacting upstream or downstream enzymes in enzymatic reactions and metabolic pathways. The resulting list of enzymes can then be integrated with transcriptomics or proteomics data via protein-protein interaction networks to perform integrative multi-omics analyses. MetaBridge was developed to be intuitive and easy to use, requiring little to no prior computational experience. The protocols described here detail all steps involved in the use of MetaBridge, from preparing input data and performing metabolite mapping to utilizing the results to build a protein-protein interaction network. © 2020 by John Wiley & Sons, Inc.</p><p><b>Basic Protocol 1</b>: Mapping metabolite data using MetaCyc identifiers</p><p><b>Basic Protocol 2</b>: Mapping metabolite data using KEGG identifiers</p><p><b>Support Protocol 1</b>: Converting compound names to HMDB IDs</p><p><b>Support Protocol 2</b>: Submitting mapped genes produced by MetaBridge for protein-protein interaction (PPI) network construction</p>","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"70 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2020-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.98","citationCount":"6","resultStr":"{\"title\":\"MetaBridge: An Integrative Multi-Omics Tool for Metabolite-Enzyme Mapping\",\"authors\":\"Travis Blimkie, Amy Huei-Yi Lee, Robert E.W. Hancock\",\"doi\":\"10.1002/cpbi.98\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p>MetaBridge is a web-based tool designed to facilitate the integration of metabolomics with other “omics” data types such as transcriptomics and proteomics. It uses data from the MetaCyc metabolic pathway database and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to map metabolite compounds to directly interacting upstream or downstream enzymes in enzymatic reactions and metabolic pathways. The resulting list of enzymes can then be integrated with transcriptomics or proteomics data via protein-protein interaction networks to perform integrative multi-omics analyses. MetaBridge was developed to be intuitive and easy to use, requiring little to no prior computational experience. The protocols described here detail all steps involved in the use of MetaBridge, from preparing input data and performing metabolite mapping to utilizing the results to build a protein-protein interaction network. © 2020 by John Wiley & Sons, Inc.</p><p><b>Basic Protocol 1</b>: Mapping metabolite data using MetaCyc identifiers</p><p><b>Basic Protocol 2</b>: Mapping metabolite data using KEGG identifiers</p><p><b>Support Protocol 1</b>: Converting compound names to HMDB IDs</p><p><b>Support Protocol 2</b>: Submitting mapped genes produced by MetaBridge for protein-protein interaction (PPI) network construction</p>\",\"PeriodicalId\":10958,\"journal\":{\"name\":\"Current protocols in bioinformatics\",\"volume\":\"70 1\",\"pages\":\"\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2020-03-21\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://sci-hub-pdf.com/10.1002/cpbi.98\",\"citationCount\":\"6\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Current protocols in bioinformatics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://onlinelibrary.wiley.com/doi/10.1002/cpbi.98\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"Biochemistry, Genetics and Molecular Biology\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Current protocols in bioinformatics","FirstCategoryId":"1085","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/cpbi.98","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"Biochemistry, Genetics and Molecular Biology","Score":null,"Total":0}
引用次数: 6
引用
批量引用
京公网安备 11010802042870号
京ICP备2023020795号-1
分享
求助内容：
应助结果提醒方式：
扫码关注我们
